first commit

README.md

+# DELLY Somatic Mutation Calling
+
+## App概述
+
+输入文件为deduped bam files。肿瘤和配对检测somatic SV，一共包括5种SV，Insertion、Deletion、Inversion、Translocation、Duplication。
+
+## 流程与参数
+
+1. DELLY检测突变
+
+```bash
+delly call -g <fastq_file> -o <output_bcf> -x human.hg38.excl.tsv <tumor_bam> <normal_bam>
+
+delly filter -f somatic -o <output_filtered_bcf> -s samples.tsv <output_bcf>
+```
+其中samples.tsv按照如下准备，其中的tumor_name和normal_name要与bam文件中一致
+
+```bash
+tumor_name	tumor
+normal_name	control
+```
+
+2. 将bcf文件转换成vcf
+
+```bash
+bcftools view <output_filtered> > <vcf>
+```
+
+## App输出文件
+
+最终的结果文件在bcf2vcf中，是一个包含了所有SV类型，经过过滤后的vcf文件

inputs

+{
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ project_name }}.fasta": "hg19_nochr.fa",
+  "{{ project_name }}.normal_bam_idx": "{{ normal_bam_idx}}",
+  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+  "{{ project_name }}.DELLYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/delly:v0.8.1",
+  "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
+  "{{ project_name }}.SMALLcluster_config": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
+  "{{ project_name }}.BCFdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
+  "{{ project_name }}.BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "{{ project_name }}.tumor_bam_idx": "{{ tumor_bam_idx }}",
+  "{{ project_name }}.SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/hg19/"
+}

tasks/bcf2vcf.wdl

+task bcf2vcf {
+	
+	File bcf
+	File bcf_index
+	String sample_name
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+
+		set -o pipefail
+		set -e
+		/opt/hall-lab/bcftools-1.9/bin/bcftools view ${bcf} > ${sample_name}.vcf
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File vcf = "${sample_name}.vcf"
+	}
+}
+
+
+
+

tasks/delly.wdl

+task delly {
+
+	File tumor_bam
+	File tumor_bam_idx
+	File normal_bam
+	File normal_bam_idx
+	File ref_dir
+	String fasta
+	String sample_name
+	String docker
+	String disk_size
+	String cluster_config
+
+	command <<<
+
+		set -o pipefail
+		set -e
+		echo -e "${sample_name}.tumor\ttumor\n${sample_name}.normal\tcontrol" > samples.tsv
+
+		nt=$(nproc)
+		export OMP_NUM_THREADS=$nt
+
+		/opt/delly/src/delly call -g ${ref_dir}/${fasta} -o ${sample_name}.delly.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam}
+
+		/opt/delly/src/delly filter -f somatic -o ${sample_name}.delly.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.somatic.bcf
+
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File bcf = "${sample_name}.delly.somatic.filtered.bcf"
+		File bcf_index = "${sample_name}.delly.somatic.filtered.bcf.csi"
+	}
+}
+
+
+
+

workflow.wdl

+
+import "./tasks/delly.wdl" as delly
+import "./tasks/bcf2vcf.wdl" as bcf2vcf
+
+workflow {{ project_name }}  {
+	
+	String SENTIEON_INSTALL_DIR
+	String SENTIEONdocker
+	String DELLYdocker
+	String BCFdocker
+
+	File tumor_bam
+	File tumor_bam_idx
+	File normal_bam
+	File normal_bam_idx
+	File ref_dir
+	String fasta
+	String sample_name
+	String disk_size
+
+	String BIGcluster_config
+	String SMALLcluster_config
+
+	call delly.delly as delly {
+		input: 
+		tumor_bam=tumor_bam,
+		tumor_bam_idx=tumor_bam_idx,
+		normal_bam=normal_bam,
+		normal_bam_idx=normal_bam_idx,
+		ref_dir=ref_dir,
+		fasta=fasta,
+		sample_name=sample_name,
+		docker=DELLYdocker,
+		disk_size=disk_size,
+		cluster_config=SMALLcluster_config
+	}
+
+	call bcf2vcf.bcf2vcf as bcf2vcf {
+		input:
+		bcf=delly.bcf,
+		bcf_index=delly.bcf_index,
+		docker=BCFdocker,
+		disk_size=disk_size,
+		cluster_config=SMALLcluster_config,
+		sample_name=sample_name
+	}
+}
+